@jbrowse/plugin-linear-genome-view 2.11.0 → 2.11.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/BaseLinearDisplay/components/LinearBlocks.js +7 -7
- package/dist/BaseLinearDisplay/components/Tooltip.js +1 -0
- package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.d.ts +17 -1
- package/dist/BaseLinearDisplay/models/BaseLinearDisplayModel.js +21 -0
- package/dist/BaseLinearDisplay/models/configSchema.d.ts +10 -0
- package/dist/BaseLinearDisplay/models/configSchema.js +15 -3
- package/dist/BaseLinearDisplay/models/serverSideRenderedBlock.js +1 -0
- package/dist/BasicTrack/index.d.ts +1 -2
- package/dist/BasicTrack/index.js +3 -2
- package/dist/FeatureTrack/index.d.ts +1 -2
- package/dist/FeatureTrack/index.js +3 -2
- package/dist/LaunchLinearGenomeView/index.d.ts +1 -2
- package/dist/LaunchLinearGenomeView/index.js +3 -2
- package/dist/LinearBareDisplay/configSchema.d.ts +5 -0
- package/dist/LinearBareDisplay/index.d.ts +1 -2
- package/dist/LinearBareDisplay/index.js +3 -2
- package/dist/LinearBareDisplay/model.d.ts +17 -2
- package/dist/LinearBasicDisplay/components/AddFiltersDialog.d.ts +10 -0
- package/dist/LinearBasicDisplay/components/AddFiltersDialog.js +94 -0
- package/dist/LinearBasicDisplay/components/{SetMaxHeight.js → SetMaxHeightDialog.js} +7 -7
- package/dist/LinearBasicDisplay/configSchema.d.ts +5 -0
- package/dist/LinearBasicDisplay/index.d.ts +1 -2
- package/dist/LinearBasicDisplay/index.js +3 -2
- package/dist/LinearBasicDisplay/model.d.ts +56 -21
- package/dist/LinearBasicDisplay/model.js +36 -5
- package/dist/LinearGenomeView/components/Cytobands.js +11 -12
- package/dist/LinearGenomeView/components/Gridlines.js +3 -4
- package/dist/LinearGenomeView/components/Highlight.js +20 -21
- package/dist/LinearGenomeView/components/OverviewScalebar.js +1 -2
- package/dist/LinearGenomeView/components/OverviewScalebarPolygon.js +2 -1
- package/dist/LinearGenomeView/components/Scalebar.js +4 -5
- package/dist/LinearGenomeView/model.d.ts +1 -0
- package/dist/LinearGenomeView/svgcomponents/SVGHeader.js +1 -1
- package/dist/LinearGenomeView/svgcomponents/SVGTrackLabel.js +1 -1
- package/dist/index.d.ts +39 -0
- package/esm/BaseLinearDisplay/components/LinearBlocks.js +7 -7
- package/esm/BaseLinearDisplay/components/Tooltip.js +1 -0
- package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.d.ts +17 -1
- package/esm/BaseLinearDisplay/models/BaseLinearDisplayModel.js +21 -0
- package/esm/BaseLinearDisplay/models/configSchema.d.ts +10 -0
- package/esm/BaseLinearDisplay/models/configSchema.js +15 -3
- package/esm/BaseLinearDisplay/models/serverSideRenderedBlock.js +1 -0
- package/esm/BasicTrack/index.d.ts +1 -2
- package/esm/BasicTrack/index.js +2 -2
- package/esm/FeatureTrack/index.d.ts +1 -2
- package/esm/FeatureTrack/index.js +2 -2
- package/esm/LaunchLinearGenomeView/index.d.ts +1 -2
- package/esm/LaunchLinearGenomeView/index.js +2 -2
- package/esm/LinearBareDisplay/configSchema.d.ts +5 -0
- package/esm/LinearBareDisplay/index.d.ts +1 -2
- package/esm/LinearBareDisplay/index.js +2 -2
- package/esm/LinearBareDisplay/model.d.ts +17 -2
- package/esm/LinearBasicDisplay/components/AddFiltersDialog.d.ts +10 -0
- package/esm/LinearBasicDisplay/components/AddFiltersDialog.js +69 -0
- package/esm/LinearBasicDisplay/components/{SetMaxHeight.js → SetMaxHeightDialog.js} +7 -7
- package/esm/LinearBasicDisplay/configSchema.d.ts +5 -0
- package/esm/LinearBasicDisplay/index.d.ts +1 -2
- package/esm/LinearBasicDisplay/index.js +2 -2
- package/esm/LinearBasicDisplay/model.d.ts +56 -21
- package/esm/LinearBasicDisplay/model.js +37 -6
- package/esm/LinearGenomeView/components/Cytobands.js +11 -12
- package/esm/LinearGenomeView/components/Gridlines.js +3 -4
- package/esm/LinearGenomeView/components/Highlight.js +20 -21
- package/esm/LinearGenomeView/components/OverviewScalebar.js +1 -2
- package/esm/LinearGenomeView/components/OverviewScalebarPolygon.js +2 -1
- package/esm/LinearGenomeView/components/Scalebar.js +4 -5
- package/esm/LinearGenomeView/model.d.ts +1 -0
- package/esm/LinearGenomeView/svgcomponents/SVGHeader.js +1 -1
- package/esm/LinearGenomeView/svgcomponents/SVGTrackLabel.js +2 -2
- package/esm/index.d.ts +39 -0
- package/package.json +2 -2
- /package/dist/LinearBasicDisplay/components/{SetMaxHeight.d.ts → SetMaxHeightDialog.d.ts} +0 -0
- /package/esm/LinearBasicDisplay/components/{SetMaxHeight.d.ts → SetMaxHeightDialog.d.ts} +0 -0
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@@ -8,7 +8,6 @@ const react_1 = __importDefault(require("react"));
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const mui_1 = require("tss-react/mui");
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const util_1 = require("@jbrowse/core/util");
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const mobx_react_1 = require("mobx-react");
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const blockTypes_1 = require("@jbrowse/core/util/blockTypes");
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const Block_1 = require("./Block");
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const useStyles = (0, mui_1.makeStyles)()({
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linearBlocks: {
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@@ -35,9 +34,10 @@ const RenderedBlocks = (0, mobx_react_1.observer)(function ({ model, }) {
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const { classes } = useStyles();
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const { blockDefinitions, blockState } = model;
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return (react_1.default.createElement(react_1.default.Fragment, null, blockDefinitions.map(block => {
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const key = `${model.id}-${block.key}`;
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if (block.type === 'ContentBlock') {
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const state = blockState.get(block.key);
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return (react_1.default.createElement(Block_1.ContentBlock, { block: block, key:
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return (react_1.default.createElement(Block_1.ContentBlock, { block: block, key: key },
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(state === null || state === void 0 ? void 0 : state.ReactComponent) ? (react_1.default.createElement(state.ReactComponent, { model: state })) : null,
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(state === null || state === void 0 ? void 0 : state.maxHeightReached) ? (react_1.default.createElement("div", { className: classes.heightOverflowed, style: {
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top: state.layout.getTotalHeight() - 16,
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@@ -45,11 +45,11 @@ const RenderedBlocks = (0, mobx_react_1.observer)(function ({ model, }) {
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height: 16,
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} }, "Max height reached")) : null));
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}
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if (block
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return
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else if (block.type === 'ElidedBlock') {
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return react_1.default.createElement(Block_1.ElidedBlock, { key: key, width: block.widthPx });
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}
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if (block
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return (react_1.default.createElement(Block_1.InterRegionPaddingBlock, { key:
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else if (block.type === 'InterRegionPaddingBlock') {
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return (react_1.default.createElement(Block_1.InterRegionPaddingBlock, { key: key, width: block.widthPx, style: { background: 'none' }, boundary: block.variant === 'boundary' }));
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}
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throw new Error(`invalid block type ${JSON.stringify(block)}`);
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})));
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@@ -40,6 +40,7 @@ const Tooltip = (0, mobx_react_1.observer)(function ({ model, clientMouseCoord,
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const y = clientMouseCoord[1];
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const { refs, floatingStyles, context } = (0, react_2.useFloating)({
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placement: 'right',
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strategy: 'fixed',
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});
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const clientPoint = (0, react_2.useClientPoint)(context, { x, y });
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const { getFloatingProps } = (0, react_2.useInteractions)([clientPoint]);
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@@ -110,6 +110,11 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
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defaultValue: string;
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contextVariable: string[];
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};
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jexlFilters: {
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type: string;
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description: string;
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defaultValue: never[];
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};
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}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
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}, {
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rendererTypeName: string;
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@@ -200,7 +205,9 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
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readonly regionTooLarge: boolean;
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readonly regionTooLargeReason: string;
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} & {
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regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features";
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regionCannotBeRenderedText(_region: import("@jbrowse/core/util").Region): "" | "Force load to see features"; /**
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* #action
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*/
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regionCannotBeRendered(_region: import("@jbrowse/core/util").Region): React.JSX.Element | null;
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} & {
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featureIdUnderMouse: string | undefined;
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* #action
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*/
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selectFeature(feature: Feature): void;
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/**
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* #action
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*/
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navToFeature(feature: Feature): void;
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/**
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* #action
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*/
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@@ -401,6 +412,11 @@ export declare const BaseLinearDisplay: import("mobx-state-tree").IModelType<{
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defaultValue: string;
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contextVariable: string[];
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};
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jexlFilters: {
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type: string;
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description: string;
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defaultValue: never[];
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};
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}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
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}>>, {
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type: string;
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@@ -36,6 +36,7 @@ const mobx_1 = require("mobx");
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const mobx_state_tree_1 = require("mobx-state-tree");
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// icons
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const MenuOpen_1 = __importDefault(require("@mui/icons-material/MenuOpen"));
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const CenterFocusStrong_1 = __importDefault(require("@mui/icons-material/CenterFocusStrong"));
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const BaseLinearDisplay_1 = require("../components/BaseLinearDisplay");
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const serverSideRenderedBlock_1 = __importDefault(require("./serverSideRenderedBlock"));
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const configSchema_1 = __importDefault(require("./configSchema"));
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@@ -211,6 +212,17 @@ function stateModelFactory() {
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session.setSelection(feature);
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}
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},
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/**
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* #action
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*/
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navToFeature(feature) {
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const view = (0, util_1.getContainingView)(self);
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view.navTo({
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refName: feature.get('refName'),
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start: feature.get('start'),
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end: feature.get('end'),
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});
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},
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/**
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* #action
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*/
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}
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},
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},
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{
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label: 'Zoom to feature',
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icon: CenterFocusStrong_1.default,
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onClick: () => {
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if (self.contextMenuFeature) {
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self.navToFeature(self.contextMenuFeature);
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}
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},
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},
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]
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: []),
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];
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defaultValue: string;
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contextVariable: string[];
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};
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/**
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* #slot
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* config jexlFilters are deferred evaluated so they are prepended with
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* jexl at runtime rather than being stored with jexl in the config
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*/
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jexlFilters: {
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description: string;
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defaultValue: never[];
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};
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}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
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export default baseLinearDisplayConfigSchema;
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/**
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* #config BaseLinearDisplay
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* #category display
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*
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* `
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*
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*
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* `BaseLinearDisplay` is a "base" config that is extended by other configs including
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* - `LinearBasicDisplay` (used for feature tracks, etc)
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* - `LinearBareDisplay` (more stripped down than even the basic display, not
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* commonly used)
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*/
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function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
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const baseLinearDisplayConfigSchema = (0, configuration_1.ConfigurationSchema)('BaseLinearDisplay', {
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defaultValue: `jexl:get(feature,'name')`,
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contextVariable: ['feature'],
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/**
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*/
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jexlFilters: {
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description: 'default set of jexl filters to apply to a track. note: these do not use the jexl prefix because they have a deferred evaluation system',
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defaultValue: [],
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},
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}, {
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/**
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package/dist/BasicTrack/index.js
CHANGED
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function BasicTrackF(pm) {
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}
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exports.default = BasicTrackF;
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function FeatureTrackF(pm) {
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function LaunchLinearGenomeViewF(pluginManager) {
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// @ts-expect-error
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async ({ session, assembly, loc, tracks = [], tracklist, nav, highlight, }) => {
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}
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exports.default = LaunchLinearGenomeViewF;
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function tryTrack(model, trackId, idsNotFound) {
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};
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export default _default;
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return new pluggableElementTypes_1.DisplayType({
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ReactComponent: BaseLinearDisplay_1.BaseLinearDisplayComponent,
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/**
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addBlock(key: string, block: import("@jbrowse/core/util/blockTypes").BaseBlock): void;
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selectFeature(feature: import("@jbrowse/core/util").Feature): void;
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navToFeature(feature: import("@jbrowse/core/util").Feature): void;
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clearFeatureSelection(): void;
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setFeatureIdUnderMouse(feature?: string | undefined): void;
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setContextMenuFeature(feature?: import("@jbrowse/core/util").Feature | undefined): void;
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jexlFilters: {
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}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>;
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}>> & import("mobx-state-tree/dist/internal").NonEmptyObject & import("mobx-state-tree")._NotCustomized, {
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type: string;
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@@ -0,0 +1,10 @@
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1
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import React from 'react';
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|
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declare const AddFiltersDialog: ({ model, handleClose, }: {
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model: {
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jexlFilters?: string[];
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activeFilters: string[];
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setJexlFilters: (arg?: string[]) => void;
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};
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handleClose: () => void;
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}) => React.JSX.Element;
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export default AddFiltersDialog;
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@@ -0,0 +1,94 @@
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"use strict";
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var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
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if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
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desc = { enumerable: true, get: function() { return m[k]; } };
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}
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Object.defineProperty(o, k2, desc);
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}) : (function(o, m, k, k2) {
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if (k2 === undefined) k2 = k;
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o[k2] = m[k];
|
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}));
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var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
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Object.defineProperty(o, "default", { enumerable: true, value: v });
|
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}) : function(o, v) {
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o["default"] = v;
|
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+
});
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|
+
var __importStar = (this && this.__importStar) || function (mod) {
|
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|
+
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|
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|
+
var result = {};
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|
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if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
|
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|
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__setModuleDefault(result, mod);
|
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|
+
return result;
|
|
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|
+
};
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|
+
Object.defineProperty(exports, "__esModule", { value: true });
|
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|
+
const react_1 = __importStar(require("react"));
|
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|
+
const mobx_react_1 = require("mobx-react");
|
|
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|
+
const ui_1 = require("@jbrowse/core/ui");
|
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|
+
const material_1 = require("@mui/material");
|
|
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|
+
const mui_1 = require("tss-react/mui");
|
|
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|
+
const jexlStrings_1 = require("@jbrowse/core/util/jexlStrings");
|
|
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|
+
const useStyles = (0, mui_1.makeStyles)()({
|
|
33
|
+
dialogContent: {
|
|
34
|
+
width: '80em',
|
|
35
|
+
},
|
|
36
|
+
textAreaFont: {
|
|
37
|
+
fontFamily: 'Courier New',
|
|
38
|
+
},
|
|
39
|
+
error: {
|
|
40
|
+
color: 'red',
|
|
41
|
+
fontSize: '0.8em',
|
|
42
|
+
},
|
|
43
|
+
});
|
|
44
|
+
function checkJexl(code) {
|
|
45
|
+
(0, jexlStrings_1.stringToJexlExpression)(code);
|
|
46
|
+
}
|
|
47
|
+
const AddFiltersDialog = (0, mobx_react_1.observer)(function ({ model, handleClose, }) {
|
|
48
|
+
const { classes } = useStyles();
|
|
49
|
+
const { activeFilters } = model;
|
|
50
|
+
const [data, setData] = (0, react_1.useState)(activeFilters.join('\n'));
|
|
51
|
+
const [error, setError] = (0, react_1.useState)();
|
|
52
|
+
(0, react_1.useEffect)(() => {
|
|
53
|
+
try {
|
|
54
|
+
data
|
|
55
|
+
.split('\n')
|
|
56
|
+
.map(line => line.trim())
|
|
57
|
+
.filter(line => !!line)
|
|
58
|
+
.map(line => checkJexl(line.trim()));
|
|
59
|
+
setError(undefined);
|
|
60
|
+
}
|
|
61
|
+
catch (e) {
|
|
62
|
+
console.error(e);
|
|
63
|
+
setError(e);
|
|
64
|
+
}
|
|
65
|
+
}, [data]);
|
|
66
|
+
return (react_1.default.createElement(ui_1.Dialog, { maxWidth: "xl", open: true, onClose: handleClose, title: "Add track filters" },
|
|
67
|
+
react_1.default.createElement(material_1.DialogContent, null,
|
|
68
|
+
react_1.default.createElement("div", null,
|
|
69
|
+
"Add filters, in jexl format, one per line, starting with the string jexl:. Examples:",
|
|
70
|
+
' ',
|
|
71
|
+
react_1.default.createElement("ul", null,
|
|
72
|
+
react_1.default.createElement("li", null,
|
|
73
|
+
react_1.default.createElement("code", null, "jexl:get(feature,'name')=='BRCA1'"),
|
|
74
|
+
" - show only feature where the name attribute is BRCA1"),
|
|
75
|
+
react_1.default.createElement("li", null,
|
|
76
|
+
react_1.default.createElement("code", null, "jexl:get(feature,'type')=='gene'"),
|
|
77
|
+
" - show only gene type features in a GFF that has many other feature types"),
|
|
78
|
+
react_1.default.createElement("li", null,
|
|
79
|
+
react_1.default.createElement("code", null, "jexl:get(feature,'score') > 400"),
|
|
80
|
+
" - show only features that have a score greater than 400"))),
|
|
81
|
+
error ? react_1.default.createElement("p", { className: classes.error }, `${error}`) : null,
|
|
82
|
+
react_1.default.createElement(material_1.TextField, { variant: "outlined", multiline: true, minRows: 5, maxRows: 10, className: classes.dialogContent, fullWidth: true, value: data, onChange: event => setData(event.target.value), InputProps: {
|
|
83
|
+
classes: {
|
|
84
|
+
input: classes.textAreaFont,
|
|
85
|
+
},
|
|
86
|
+
} })),
|
|
87
|
+
react_1.default.createElement(material_1.DialogActions, null,
|
|
88
|
+
react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", type: "submit", autoFocus: true, disabled: !!error, onClick: () => {
|
|
89
|
+
model.setJexlFilters(data.split('\n'));
|
|
90
|
+
handleClose();
|
|
91
|
+
} }, "Submit"),
|
|
92
|
+
react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel"))));
|
|
93
|
+
});
|
|
94
|
+
exports.default = AddFiltersDialog;
|
|
@@ -40,12 +40,12 @@ const SetMaxHeightDialog = (0, mobx_react_1.observer)(function ({ model, handleC
|
|
|
40
40
|
return (react_1.default.createElement(ui_1.Dialog, { open: true, onClose: handleClose, title: "Set max height" },
|
|
41
41
|
react_1.default.createElement(material_1.DialogContent, { className: classes.root },
|
|
42
42
|
react_1.default.createElement(material_1.Typography, null, "Set max height for the track. For example, you can increase this if the layout says \"Max height reached\""),
|
|
43
|
-
react_1.default.createElement(material_1.TextField, { value: max, onChange: event => setMax(event.target.value), placeholder: "Enter max score" }),
|
|
44
|
-
|
|
45
|
-
|
|
46
|
-
|
|
47
|
-
|
|
48
|
-
|
|
49
|
-
|
|
43
|
+
react_1.default.createElement(material_1.TextField, { value: max, onChange: event => setMax(event.target.value), placeholder: "Enter max score" })),
|
|
44
|
+
react_1.default.createElement(material_1.DialogActions, null,
|
|
45
|
+
react_1.default.createElement(material_1.Button, { variant: "contained", color: "primary", type: "submit", autoFocus: true, onClick: () => {
|
|
46
|
+
model.setMaxHeight(max !== '' && !Number.isNaN(+max) ? +max : undefined);
|
|
47
|
+
handleClose();
|
|
48
|
+
} }, "Submit"),
|
|
49
|
+
react_1.default.createElement(material_1.Button, { variant: "contained", color: "secondary", onClick: () => handleClose() }, "Cancel"))));
|
|
50
50
|
});
|
|
51
51
|
exports.default = SetMaxHeightDialog;
|
|
@@ -30,5 +30,10 @@ declare function configSchemaFactory(pluginManager: PluginManager): import("@jbr
|
|
|
30
30
|
defaultValue: string;
|
|
31
31
|
contextVariable: string[];
|
|
32
32
|
};
|
|
33
|
+
jexlFilters: {
|
|
34
|
+
type: string;
|
|
35
|
+
description: string;
|
|
36
|
+
defaultValue: never[];
|
|
37
|
+
};
|
|
33
38
|
}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, "displayId">>, undefined>>;
|
|
34
39
|
export default configSchemaFactory;
|
|
@@ -1,5 +1,4 @@
|
|
|
1
1
|
import PluginManager from '@jbrowse/core/PluginManager';
|
|
2
|
-
|
|
3
|
-
export default _default;
|
|
2
|
+
export default function LinearBasicDisplay(pluginManager: PluginManager): void;
|
|
4
3
|
export { default as modelFactory } from './model';
|
|
5
4
|
export { default as configSchema } from './configSchema';
|
|
@@ -9,7 +9,7 @@ const BaseLinearDisplay_1 = require("../BaseLinearDisplay");
|
|
|
9
9
|
// locals
|
|
10
10
|
const configSchema_1 = __importDefault(require("./configSchema"));
|
|
11
11
|
const model_1 = __importDefault(require("./model"));
|
|
12
|
-
|
|
12
|
+
function LinearBasicDisplay(pluginManager) {
|
|
13
13
|
pluginManager.addDisplayType(() => {
|
|
14
14
|
const config = (0, configSchema_1.default)(pluginManager);
|
|
15
15
|
return new pluggableElementTypes_1.DisplayType({
|
|
@@ -22,7 +22,8 @@ exports.default = (pluginManager) => {
|
|
|
22
22
|
ReactComponent: BaseLinearDisplay_1.BaseLinearDisplayComponent,
|
|
23
23
|
});
|
|
24
24
|
});
|
|
25
|
-
}
|
|
25
|
+
}
|
|
26
|
+
exports.default = LinearBasicDisplay;
|
|
26
27
|
var model_2 = require("./model");
|
|
27
28
|
Object.defineProperty(exports, "modelFactory", { enumerable: true, get: function () { return __importDefault(model_2).default; } });
|
|
28
29
|
var configSchema_2 = require("./configSchema");
|